Multiple sequence alignment - TraesCS5A01G457600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G457600 chr5A 100.000 4022 0 0 1 4022 637454894 637458915 0.000000e+00 7428.0
1 TraesCS5A01G457600 chr5A 100.000 29 0 0 3237 3265 637458024 637458052 2.000000e-03 54.7
2 TraesCS5A01G457600 chr5A 100.000 29 0 0 3131 3159 637458130 637458158 2.000000e-03 54.7
3 TraesCS5A01G457600 chr2A 97.021 3290 80 7 31 3309 49454071 49450789 0.000000e+00 5517.0
4 TraesCS5A01G457600 chr2A 96.348 712 23 3 3311 4022 49450701 49449993 0.000000e+00 1168.0
5 TraesCS5A01G457600 chr2A 100.000 29 0 0 3131 3159 49450865 49450837 2.000000e-03 54.7
6 TraesCS5A01G457600 chr2A 100.000 29 0 0 3237 3265 49450971 49450943 2.000000e-03 54.7
7 TraesCS5A01G457600 chr3A 96.737 3126 74 8 1 3120 57568595 57571698 0.000000e+00 5182.0
8 TraesCS5A01G457600 chr3A 96.788 716 17 3 3311 4022 57585400 57586113 0.000000e+00 1190.0
9 TraesCS5A01G457600 chr3A 94.898 196 6 1 3118 3309 57585117 57585312 1.820000e-78 303.0
10 TraesCS5A01G457600 chr3A 100.000 29 0 0 3237 3265 57585130 57585158 2.000000e-03 54.7
11 TraesCS5A01G457600 chr1B 87.253 2730 302 30 1 2721 646867765 646870457 0.000000e+00 3072.0
12 TraesCS5A01G457600 chr1B 83.406 687 101 11 3312 3994 646871097 646871774 3.410000e-175 625.0
13 TraesCS5A01G457600 chr4A 83.431 2378 346 32 549 2899 663312524 663314880 0.000000e+00 2165.0
14 TraesCS5A01G457600 chr4A 84.278 388 60 1 98 484 663311782 663312169 1.060000e-100 377.0
15 TraesCS5A01G457600 chr4A 84.255 235 34 3 2895 3127 663315772 663316005 4.040000e-55 226.0
16 TraesCS5A01G457600 chr7D 85.551 1841 239 18 1 1829 638557902 638556077 0.000000e+00 1901.0
17 TraesCS5A01G457600 chr7D 82.925 1265 191 15 1894 3153 638555976 638554732 0.000000e+00 1116.0
18 TraesCS5A01G457600 chr2B 88.910 1064 108 4 668 1722 453994570 453995632 0.000000e+00 1303.0
19 TraesCS5A01G457600 chrUn 83.471 484 76 3 1 483 10118823 10119303 7.930000e-122 448.0
20 TraesCS5A01G457600 chr6D 81.139 281 53 0 1912 2192 26661377 26661097 4.040000e-55 226.0
21 TraesCS5A01G457600 chr5B 82.659 173 30 0 2297 2469 74335575 74335403 1.940000e-33 154.0
22 TraesCS5A01G457600 chr5B 81.188 101 13 5 1679 1776 42180419 42180516 4.310000e-10 76.8
23 TraesCS5A01G457600 chr3D 74.554 224 42 12 1355 1573 419870997 419870784 2.580000e-12 84.2
24 TraesCS5A01G457600 chr3D 100.000 32 0 0 2146 2177 512860893 512860862 4.340000e-05 60.2
25 TraesCS5A01G457600 chr1A 80.769 104 14 5 1679 1779 21634217 21634117 4.310000e-10 76.8
26 TraesCS5A01G457600 chr1A 81.188 101 13 5 1679 1776 573954707 573954804 4.310000e-10 76.8
27 TraesCS5A01G457600 chr3B 71.672 293 71 12 1355 1641 578622487 578622201 2.010000e-08 71.3
28 TraesCS5A01G457600 chr4B 89.091 55 6 0 1410 1464 476946320 476946266 7.210000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G457600 chr5A 637454894 637458915 4021 False 2512.466667 7428 100.000000 1 4022 3 chr5A.!!$F1 4021
1 TraesCS5A01G457600 chr2A 49449993 49454071 4078 True 1698.600000 5517 98.342250 31 4022 4 chr2A.!!$R1 3991
2 TraesCS5A01G457600 chr3A 57568595 57571698 3103 False 5182.000000 5182 96.737000 1 3120 1 chr3A.!!$F1 3119
3 TraesCS5A01G457600 chr3A 57585117 57586113 996 False 515.900000 1190 97.228667 3118 4022 3 chr3A.!!$F2 904
4 TraesCS5A01G457600 chr1B 646867765 646871774 4009 False 1848.500000 3072 85.329500 1 3994 2 chr1B.!!$F1 3993
5 TraesCS5A01G457600 chr4A 663311782 663316005 4223 False 922.666667 2165 83.988000 98 3127 3 chr4A.!!$F1 3029
6 TraesCS5A01G457600 chr7D 638554732 638557902 3170 True 1508.500000 1901 84.238000 1 3153 2 chr7D.!!$R1 3152
7 TraesCS5A01G457600 chr2B 453994570 453995632 1062 False 1303.000000 1303 88.910000 668 1722 1 chr2B.!!$F1 1054

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
930 1230 1.081892 GCAAGCTGATGACGATGTGT 58.918 50.0 0.0 0.0 0.00 3.72 F
1170 1489 0.392998 AGAGTGTGCTTTATGCGGGG 60.393 55.0 0.0 0.0 46.63 5.73 F
1174 1493 0.540830 TGTGCTTTATGCGGGGGTTT 60.541 50.0 0.0 0.0 46.63 3.27 F
1176 1495 0.605589 TGCTTTATGCGGGGGTTTTG 59.394 50.0 0.0 0.0 46.63 2.44 F
2098 2472 0.741915 GGTTCAAGTGCCGGTTTGAA 59.258 50.0 19.9 19.9 40.06 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2279 1.064758 AGGTGTTCACCTTCAGCACAA 60.065 47.619 17.56 0.0 36.56 3.33 R
2069 2443 2.288666 GCACTTGAACCACTTCTCACA 58.711 47.619 0.00 0.0 0.00 3.58 R
2395 2771 2.435938 GAAAGTGGGCGCATCCGA 60.436 61.111 10.83 0.0 36.29 4.55 R
2692 3068 2.490351 CCTGGCTAATTGGAGGATGCAT 60.490 50.000 0.00 0.0 35.22 3.96 R
3398 4787 1.149361 CTCTCTCGCTCGAGTACGCT 61.149 60.000 15.13 0.0 42.49 5.07 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 3.562609 GGTTGGATGGGTTAGCAGGTAAA 60.563 47.826 0.00 0.00 0.00 2.01
196 198 1.450531 CCGGCTGGCCTGATTTGATC 61.451 60.000 14.77 0.00 0.00 2.92
546 845 4.820897 TGTTACCATGTTGTTTGTTGCAA 58.179 34.783 0.00 0.00 0.00 4.08
603 903 4.102367 AGGGCAAACCAAAAGAAGCAAATA 59.898 37.500 0.00 0.00 43.89 1.40
678 978 1.346395 ACGAAGGCTGGTACATCAACA 59.654 47.619 0.00 0.00 38.20 3.33
930 1230 1.081892 GCAAGCTGATGACGATGTGT 58.918 50.000 0.00 0.00 0.00 3.72
990 1290 3.057019 GACAGCGAGTTCACATACAACA 58.943 45.455 0.00 0.00 0.00 3.33
1084 1389 2.642139 TGACGTTATCACCTTCGACC 57.358 50.000 0.00 0.00 29.99 4.79
1166 1485 5.702865 TCATTTTCAGAGTGTGCTTTATGC 58.297 37.500 0.00 0.00 43.25 3.14
1167 1486 3.811722 TTTCAGAGTGTGCTTTATGCG 57.188 42.857 0.00 0.00 46.63 4.73
1168 1487 1.725641 TCAGAGTGTGCTTTATGCGG 58.274 50.000 0.00 0.00 46.63 5.69
1169 1488 0.729116 CAGAGTGTGCTTTATGCGGG 59.271 55.000 0.00 0.00 46.63 6.13
1170 1489 0.392998 AGAGTGTGCTTTATGCGGGG 60.393 55.000 0.00 0.00 46.63 5.73
1171 1490 1.376609 GAGTGTGCTTTATGCGGGGG 61.377 60.000 0.00 0.00 46.63 5.40
1172 1491 1.677633 GTGTGCTTTATGCGGGGGT 60.678 57.895 0.00 0.00 46.63 4.95
1173 1492 1.075836 TGTGCTTTATGCGGGGGTT 59.924 52.632 0.00 0.00 46.63 4.11
1174 1493 0.540830 TGTGCTTTATGCGGGGGTTT 60.541 50.000 0.00 0.00 46.63 3.27
1175 1494 0.606096 GTGCTTTATGCGGGGGTTTT 59.394 50.000 0.00 0.00 46.63 2.43
1176 1495 0.605589 TGCTTTATGCGGGGGTTTTG 59.394 50.000 0.00 0.00 46.63 2.44
1177 1496 0.892063 GCTTTATGCGGGGGTTTTGA 59.108 50.000 0.00 0.00 0.00 2.69
1178 1497 1.480545 GCTTTATGCGGGGGTTTTGAT 59.519 47.619 0.00 0.00 0.00 2.57
1668 2007 1.609208 AATTCTGTGCTCGCCAAACT 58.391 45.000 0.00 0.00 0.00 2.66
1905 2279 6.773976 TTTTTCTTCCAAACAGAGTCATGT 57.226 33.333 0.00 0.00 33.96 3.21
1957 2331 6.982852 AGTACACGCAAGCAAGATATATACT 58.017 36.000 0.00 0.00 45.62 2.12
2058 2432 4.386867 AATACATAGTGACACACCGGAG 57.613 45.455 9.46 1.26 34.49 4.63
2098 2472 0.741915 GGTTCAAGTGCCGGTTTGAA 59.258 50.000 19.90 19.90 40.06 2.69
2111 2485 3.117794 CGGTTTGAAGTCAACGTGTCTA 58.882 45.455 0.00 0.00 35.28 2.59
2195 2569 3.570975 TCACTCGCTACAGGTTAGTTTCA 59.429 43.478 0.00 0.00 0.00 2.69
2246 2620 5.712217 TGATAGGTGCTTTATTTTCGACG 57.288 39.130 0.00 0.00 0.00 5.12
2480 2856 2.747855 CAGGAACCCGGCAGCTTC 60.748 66.667 0.00 0.00 0.00 3.86
2614 2990 2.159156 GGCGGTCCAAACTCAAAGTTTT 60.159 45.455 2.42 0.00 45.38 2.43
2692 3068 1.138883 GATGCCGCGTCTGTGTCTA 59.861 57.895 4.92 0.00 0.00 2.59
2762 3138 6.378280 GGTGATGGGTACAATTCAGATTTCTT 59.622 38.462 0.00 0.00 0.00 2.52
2947 4223 1.001764 CCAGCACTTGCCCTGATCA 60.002 57.895 0.00 0.00 43.38 2.92
3161 4438 5.011090 ACGTATCTAGATGCACATGTGTT 57.989 39.130 26.01 14.65 0.00 3.32
3309 4612 9.922305 CTTCGAAATGTAGGAATTCATAACTTC 57.078 33.333 7.93 7.26 0.00 3.01
3449 4842 0.680921 CATTTGCCCGGAGACACCAT 60.681 55.000 0.73 0.00 38.90 3.55
3498 4891 1.403814 CCCGTCTCTTCCTCTGCATA 58.596 55.000 0.00 0.00 0.00 3.14
3873 5267 1.468224 CCATCTGTCGACCGACTCTTG 60.468 57.143 21.01 14.81 44.80 3.02
3920 5314 2.808315 CTCATGGGAGGACGACGG 59.192 66.667 0.00 0.00 37.51 4.79
4006 5400 1.229529 CTGTACTCACCCCCACCCT 60.230 63.158 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 1.072965 CAGAGAAGCAGGAAACAGGGT 59.927 52.381 0.00 0.00 0.00 4.34
150 151 5.293079 GGTATGAGCTAAAACAGAGAAGCAG 59.707 44.000 0.00 0.00 37.44 4.24
546 845 9.737844 AATAACCAACCAAAATGCATTTAGATT 57.262 25.926 24.35 15.13 0.00 2.40
603 903 4.245660 CATTGACACCATGTAGACTTCGT 58.754 43.478 0.00 0.00 0.00 3.85
678 978 3.772025 TGGTTGTGTTTGGACCTGAATTT 59.228 39.130 0.00 0.00 34.52 1.82
990 1290 5.420421 CCGTATCCTCATCATCTACCTGAAT 59.580 44.000 0.00 0.00 0.00 2.57
1084 1389 4.561735 ACAGGTTTGTTTTGTATGTCGG 57.438 40.909 0.00 0.00 32.28 4.79
1165 1484 3.051392 CTCGCATCAAAACCCCCGC 62.051 63.158 0.00 0.00 0.00 6.13
1166 1485 1.376683 TCTCGCATCAAAACCCCCG 60.377 57.895 0.00 0.00 0.00 5.73
1167 1486 1.644786 CGTCTCGCATCAAAACCCCC 61.645 60.000 0.00 0.00 0.00 5.40
1168 1487 0.672401 TCGTCTCGCATCAAAACCCC 60.672 55.000 0.00 0.00 0.00 4.95
1169 1488 0.721718 CTCGTCTCGCATCAAAACCC 59.278 55.000 0.00 0.00 0.00 4.11
1170 1489 1.390463 GTCTCGTCTCGCATCAAAACC 59.610 52.381 0.00 0.00 0.00 3.27
1171 1490 1.390463 GGTCTCGTCTCGCATCAAAAC 59.610 52.381 0.00 0.00 0.00 2.43
1172 1491 1.710013 GGTCTCGTCTCGCATCAAAA 58.290 50.000 0.00 0.00 0.00 2.44
1173 1492 0.456142 CGGTCTCGTCTCGCATCAAA 60.456 55.000 0.00 0.00 0.00 2.69
1174 1493 1.136774 CGGTCTCGTCTCGCATCAA 59.863 57.895 0.00 0.00 0.00 2.57
1175 1494 1.706287 CTCGGTCTCGTCTCGCATCA 61.706 60.000 0.00 0.00 37.69 3.07
1176 1495 1.010574 CTCGGTCTCGTCTCGCATC 60.011 63.158 0.00 0.00 37.69 3.91
1177 1496 2.473760 CCTCGGTCTCGTCTCGCAT 61.474 63.158 0.00 0.00 37.69 4.73
1178 1497 2.871216 ATCCTCGGTCTCGTCTCGCA 62.871 60.000 0.00 0.00 37.69 5.10
1319 1657 2.033448 GTCATGCACCCGGTTGGA 59.967 61.111 0.00 0.00 37.49 3.53
1668 2007 0.251787 TCTCACTCCTGCCAGTGCTA 60.252 55.000 3.26 0.00 43.18 3.49
1887 2227 4.790766 GCACAACATGACTCTGTTTGGAAG 60.791 45.833 0.00 0.00 37.25 3.46
1888 2228 3.066621 GCACAACATGACTCTGTTTGGAA 59.933 43.478 0.00 0.00 37.25 3.53
1905 2279 1.064758 AGGTGTTCACCTTCAGCACAA 60.065 47.619 17.56 0.00 36.56 3.33
1957 2331 7.039784 CCACCAAAAATCTCAAACATCTTCCTA 60.040 37.037 0.00 0.00 0.00 2.94
2069 2443 2.288666 GCACTTGAACCACTTCTCACA 58.711 47.619 0.00 0.00 0.00 3.58
2098 2472 5.221581 ACCAAGGTTATTAGACACGTTGACT 60.222 40.000 6.36 0.00 39.89 3.41
2195 2569 4.955925 TTGATCATAAAAATGGTCGCGT 57.044 36.364 5.77 0.00 34.50 6.01
2246 2620 7.137490 TCATCATGAAGACAATTGTGAAGTC 57.863 36.000 17.58 7.99 0.00 3.01
2393 2769 3.545124 AAAGTGGGCGCATCCGACA 62.545 57.895 10.83 0.00 46.86 4.35
2395 2771 2.435938 GAAAGTGGGCGCATCCGA 60.436 61.111 10.83 0.00 36.29 4.55
2480 2856 3.875727 CAGGCCTGTCATCATAAACTCAG 59.124 47.826 25.53 0.00 0.00 3.35
2685 3061 4.508551 AATTGGAGGATGCATAGACACA 57.491 40.909 0.00 0.00 35.22 3.72
2692 3068 2.490351 CCTGGCTAATTGGAGGATGCAT 60.490 50.000 0.00 0.00 35.22 3.96
2831 3207 3.253838 TAGTGGTTGGCCCGCCTT 61.254 61.111 13.05 5.25 45.49 4.35
2947 4223 4.965283 TCCTTTTTGGGGATATCACCTT 57.035 40.909 24.51 0.00 41.04 3.50
2997 4273 4.974438 TCGGTGCCCTGGAACCCT 62.974 66.667 7.81 0.00 40.81 4.34
3161 4438 2.812358 ACGTATGTTCAGACAGCACA 57.188 45.000 0.00 0.00 39.58 4.57
3398 4787 1.149361 CTCTCTCGCTCGAGTACGCT 61.149 60.000 15.13 0.00 42.49 5.07
3498 4891 5.404946 GCATGTAGCAACAAAGAATGTGAT 58.595 37.500 0.00 0.00 42.99 3.06
3711 5105 4.106341 TCCTTTCTTTCAATCTCCCTTGGT 59.894 41.667 0.00 0.00 0.00 3.67
3920 5314 2.970974 GCAAGGCTGTCAACCTCGC 61.971 63.158 0.00 0.00 36.14 5.03


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.